University of Groningen Molecular Ensemble Junctions Soni
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University of Groningen Molecular Ensemble Junctions Soni, Saurabh DOI: 10.33612/diss.177486717 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2021 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Soni, S. (2021). Molecular Ensemble Junctions: a combined experimental & theoretical investigation. University of Groningen. https://doi.org/10.33612/diss.177486717 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 28-03-2022
University of Groningen Molecular Ensemble Junctions Soni
DOI: 10.33612/diss.177486717
IMPORTANT NOTE: You are advised to consult the publisher's version
(publisher's PDF) if you wish to cite from it. Please check the
document version below.
Document Version Publisher's PDF, also known as Version of
record
Publication date: 2021
Link to publication in University of Groningen/UMCG research
database
Citation for published version (APA): Soni, S. (2021). Molecular
Ensemble Junctions: a combined experimental & theoretical
investigation. University of Groningen.
https://doi.org/10.33612/diss.177486717
Copyright Other than for strictly personal use, it is not permitted
to download or to forward/distribute the text or part of it without
the consent of the author(s) and/or copyright holder(s), unless the
work is under an open content license (like Creative
Commons).
The publication may also be distributed here under the terms of
Article 25fa of the Dutch Copyright Act, indicated by the “Taverne”
license. More information can be found on the University of
Groningen website:
https://www.rug.nl/library/open-access/self-archiving-pure/taverne-
amendment.
Take-down policy If you believe that this document breaches
copyright please contact us providing details, and we will remove
access to the work immediately and investigate your claim.
Downloaded from the University of Groningen/UMCG research database
(Pure): http://www.rug.nl/research/portal. For technical reasons
the number of authors shown on this cover page is limited to 10
maximum.
Download date: 28-03-2022
INTERFERENCE
Abstract: Understanding the role and relevance of quantum
interference (QI) in molecu- lar junctions for Molecular
Electronics devices has been long sought after. Translating
molecular features, that are responsible for destructive QI, into
an observable like tun- neling current in devices with molecules as
the core element builds up the prospect of fu- ture applications.
Starting with establishing the origin of QI in tunneling junction,
here we discuss four series of molecular wires in which we
manipulate QI using their elec- tronic structure properties. Using
ab-initio density functional theory calculations com- bined with
non-equilibrium green’s function approach, we calculate
transmission spectra to study the effects of electron-donating and
withdrawing functional groups on the shape, size, and position of
QI feature in anthraquinoid-core-based wires; as well explain the
two-terminal, QI-induced memory behavior in tetracyanoquinone based
molecular junc- tion. Finally, we elucidate on the collective and
individual roles of bond-topology and quinoid functional groups in
the molecular wire series based on benzodithiophene and
thienothiophene cores.
The contents of this chapter are also published as part of the
following publications: (i) Results in sec- tion 3.4 are included
in M. Carlotti, S. Soni, X. Qiu, E. Sauter, M. Zharnikov, R. C.
Chiechi, Nanoscale Adv. 2019, 1, 2018–2028 doi: 10.1039/C8NA00223A
(ii) Results in subsection 3.4.1 are included in M. Carlotti, S.
Soni, S. Kumar, Y. Ai, E. Sauter, M. Zharnikov, R. C. Chiechi,
Angew. Chem. Int. Ed. 2018, 57, 15681 doi: 10.1002/anie.201807879
(iii) Results in section 3.5 are included in Y. Zhang, G. Ye, S.
Soni, X. Qiu, T. L. Krijger, H. T. Jonkman, M. Carlotti, E. Sauter,
M. Zharnikov, R. C. Chiechi, Chem. Sci. 2018, 9, 4414–4423 doi:
10.1039/C8SC00165K. I would like to thank the contributions of the
following collaborators whose crucial work is included in this
chapter in the form of supporting data: Dr. Y. Zhang, Dr. G. Ye,
Dr. X. Qiu, and Dr. M. Carlotti.
3.1. INTRODUCTION Structure-function relationships have inspired
several branches of scientific research in- cluding molecular
electronics (ME). Several molecular devices are based on ME func-
tionalities, such as molecular switches, rectifiers, transistors,
quantum interference, etc., and have potential applications.
However, developing more practical systems requires a further
understanding of the underlying principles in manipulating and
controlling these functions. Quantum interference (QI) has shown
importance in mesoscopic elec- tronic systems[1] where two electron
waves can interfere constructively or destructively depending on
the phase difference between the two. QI is a collection of
phenomena re- lated to Fermions whose wave functions can interfere
with themselves in molecular tun- neling junctions (MTJ), as
explained in section 3.2. Destructive QI can lower the trans-
mission probability between the electrodes, significantly lowering
conductance without altering the tunneling distance in most
cases.
In MTJ, π-conjugated molecules influence tunneling transport in a
more non-trivial fashion, rather than posing as a simple,
rectangular tunneling barrier. When the pres- ence of different,
highly-coupled pathways in a molecular system affect the
conductance due to the change in bond-topology, it is typically
ascribed to QI,[2] which was originally adapted from the
Ehrenberg–Siday–Aharonov–Bohm effect[3,4] to substituted benzenes
(section 3.2).[5,6] Solomon et al. further refined the concept in
the context of ME where it is now well established that destructive
QI suppresses the tunneling probability of tra- versing electron
wave, lowering the conductance of the MTJ.[7–13] Experimental
evidence of QI has been demonstrated in several experimental
platforms with different device geometries and different molecular
systems in molecular electronics.[2,5,6,10,14,15] Not- able
categories where QI plays a major role include para and meta
connections,[5,6,16–24]
varied connectivity in azulene,[25–27] linear versus
cross-conjugation,[13,14,28–31] through- space QI,[32–34] and
σ-framework QI.[35–37]
Several applications based on QI has shown potential as an
intriguing ME element,[38] such as gating via heteroatom
substitution,[29,39,40] electrochemical gating,[41] switching using
acid and base,,[27,42] two-terminal molecular memory,[43] and
parallel-pathways control and manipulation.[42,44–46] The concept
“quantum interfer- ence effect transistor” was proposed long ago
using meta-benzene structures for device application[47] and lately
functioning of a QI-based transistor, consisting of paracyclo-
phane core, was also demonstrated.[48]
In this chapter, I will discuss the results of our Density
Functional Theory simulations combined with Non-Equilibrium Green’s
Function approach for computing transport properties on a series of
conjugated molecular wires – with different cores, incorporat- ing
functional groups, and manipulating bond-topology – as ideal
systems to study QI in large-area EGaIn MTJ, as shown in Figure
3.1.[14,28,43,49] However, before that, I will discuss the origin
of QI in MTJ in section 3.2. In section 3.3, I first elucidate on
destruct- ive QI in the conjugated and rigid molecular wires AC,
AH, and AQ (see Figure 3.1b) that have served as benchmarks since
their first reports.[14,50–52] In section 3.4, I study the ma-
nipulation of QI feature when the cross-conjugated molecular wire
AQ is functionalized by different electron-donating and withdrawing
groups. In subsection 3.4.1, I discuss the transmission spectra of
different redox states of a unique derivative of AQ – TCNAQ – which
has cyano groups at the two carbonyl positions, showing plausible
application
3
47
INTERFERENCE
Figure 3.1 (a) Schematic of a MTJ comprising bottom electrode as
either AuTS or AuMica, self-assembled mono- layers of molecular
wires with the “arms” that are linearly-conjugated phenylacetylenes
with varying aryl group (Ar) in the core, and Ga2O3//EGaIn as the
top electrode. Molecular cores (Ar) for all the molecular wires
stud- ied in this chapter: (b) AC, AH, and AQ benchmark series; (c)
several derivatives of AQ molecular wire syn- thesized by
functionalizing the carbonyl position with different functional
group, including TCNAQ which has been demonstrated as a
redox-active QI switch (AMe, A(CH2), AF, A(Alk), and A(All) were
not synthetically ac- cessible but were investigated in silico);
(d) BDT-n series (n = 1−3) for untangling the effect of quinones
and bond-topology on QI, along with other 3 derivatives that were
only investigated in silico; (e) Bithiophene (BT as control) and
fused thienothiophenes molecules (TT-n; n = 1− 3) for further
studying the effect of bond- topology on QI.
as a molecular memory. Further, in section 3.5, I report
transmission calculations on a molecular series based on
benzodithiophene core that helps us isolate the effects of
cross-conjugated bond-topology and electron-withdrawing quinone
groups on QI. Fi- nally, in subsection 3.5.1, I present simulations
and discuss transmission probabilities of molecular wires with
thienothiophene core affecting bond-topology and destructive QI in
the process.
3.2. ORIGIN OF QUANTUM INTERFERENCE
Describing destructive QI in molecular systems is non-trivial.
Owing to its quantum- mechanical nature, a physical description of
QI can be confusing and misleading if not handled with caution. I
will describe the origin and adaptation of QI in ME but, if
in-
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48
3.2. ORIGIN OF QUANTUM INTERFERENCE
terested in detailed reading and formalism of different QI-based
concepts, the reader is encouraged to refer to further pedagogical
and research texts.[1,2,53,54]
To understand the complexity of this phenomenon, we will first take
a step back and recall the classical analogue which served as an
inspiration: the famous double- slit experiment performed by the
eminent physicist Thomas Young in 1801 investigating the nature of
light.[55] Young demonstrated that a beam of monochromatic light
upon passing through two closely-spaced slits would create an
interference pattern upon re- combination, as shown in Figure 3.2.
In Young’s experiment, wherever two peaks or two troughs (i.e.,
in-phase waves) met, they interfered constructively, resulting in a
bright spot; whereas the recombination of a peak and trough
(out-of-phase waves) canceled each other (interfering
destructively), resulting in a dark spot. However, the quantum-
mechanical nature of tunneling electrons makes this analogy
inapt—even though it provides a good initial understanding of wave
interference—so we move on to meso- scopic ring systems. It was
demonstrated that when an electron beam is split around a solenoid,
the wavefunctions of the two electron waves experience a
phase-shift pro- portional to the magnitude of magnetic flux in the
solenoid.[56,57] As a result, the elec- tron beams upon
recombination interfere constructively or destructively depending
on the phase difference, which is named as
Ehrenberg–Siday–Aharonov–Bohm effect.[3,4]
The effect was also demonstrated in normal-metal rings.[58]
Naturally, it is tempting to apply this concept to cyclic molecules
like para- and meta-substituted benzene rings (Figure 3.2). While
para-substituted benzene provides two symmetrical pathways (i.e., φ
= 0), meta-connected benzene presents asymmetric pathway consisting
of 2 and 4 sp-carbons each (i.e., φ 6= 0). It has been predicted
theoretically and shown exper- imentally that meta-benzene is few
orders of magnitude lower in conductance com- pared to
para-benzene. This path-difference (translating into
phase-difference), there- fore, could be considered as a reason for
destructive QI in the meta-benzene case.[20]
This analogy, however, breaks down for acyclic systems such as
alkenes,[8] more complex systems with through-space QI,[34,59]
larger aromatic ring systems,[16,28] and for systems with
σ-QI,[35,37] also shown in Figure 3.2. Therefore, neither of the
above two phenom- ena can be considered an explanation or QI
analogues in MTJ. Furthermore, in Young’s double-slit and
Aharonov-Bohm experiments, two waves interfere with one another,
but for tunneling transport across molecules, the electron
interferes with itself as its wave- function gets ‘scattered’ by
the tunneling barrier defined by the molecular bridge. There- fore,
we will now move away from the interference analogy of the two
experiments to a more quantum-mechanical description from the point
of view of molecules and their eigenstates.
Isolated molecules have discrete energy levels, just like
individual atoms and quantum dots. Even though these energy modes
are perturbed when they are anchored to metal electrodes
(especially when the molecule is directly conjugated to the metal),
their contribution adds up to the overall transmission probability
(T (E)) of the tunnel- ing electron. The contribution will vary for
different eigenmodes, hence, the peaks in the transmission can be
decomposed by projecting the molecular conductance orbitals from
the transport calculation onto the molecular orbitals from fragment
DFT calcula- tions, as described earlier in the literature.[9,54]
To perceive the difference between the molecular conductance
orbitals and molecular orbitals, it helps to realize that both
be-
3
49
INTERFERENCE
0
0
Figure 3.2 Schematic showing the evolution of quantum interference
phenomenon from wave interference in classical and
quantum-mechanical analogues to interference in MTJ. The first
panel sketches Young’s double- slit experiment demonstrating
interference pattern originating from traveling waves passing
through two nar- row slits[55] and the Aharonov-Bohm effect where
the wavefunctions of the two electron beams experience a
phase-shift proportional to the magnetic flux in the center, giving
rise to an interference pattern upon re- combination. The second
panel highlights the concept of path-difference between the two
available physical pathways for electron traversing across a para-
and meta-benzenedithiol in a tunneling junction. The third panel
shows examples of molecules in which the analogy of multiple
pathways fails as they induce destruct- ive QI via
cross-conjugation, through-space, or by sigma framework. The last
panel shows an energy diagram of a metal-molecule-metal junction,
showing several factors that can govern the total electron
transmission, which is the contribution of individual transmissions
through these several energetic pathways over the same physical
pathway, such as, fermi levels (EFermi) of the two electrodes,
energy levels of the molecular bridge, and coupling of molecular
levels to the electrodes (ΓL/R ).
3
50
3.3. THE BENCHMARKS: AC, AH, AND AQ SERIES
come the same in the limiting case when the molecule-electrode
coupling becomes zero. The simplest system which would give rise to
a perfect antiresonance QI dip (T (E) → 0) will be the one in which
the contribution of two molecular conductance orbitals dif- fer by
a phase of π. This scenario naturally becomes more complicated when
we take into account a complete molecule and combination of all the
involved eigenstates. Al- though several molecular orbitals
contribute to a transmission peak, generally speaking, the ones in
the vicinity of the peak in an energy landscape, will contribute
the most. For instance, resonance peaks in transmission spectra,
where the T (E) → 1, are usually located in the vicinity of the
energies of molecular levels. Similarly, the destructive QI
feature, which is usually identified in form of a sharp
antiresonance dip in the trans- mission spectra (T (E) → 0), is
usually located around the energy levels which contrib- ute the
most towards its origin. The molecular conductance orbitals could
be deloc- alised over the same molecular backbone or separated on
different fragments. Thus, the origin of the destructive QI is
attributed to the sum of out-of-phase contributions from different
energy states spanning the same or neighboring physical pathway on
the molecule. This is in contrast to the classical analogue of the
double-slit experiment or quantum-mechanical analogue of the
Ehrenberg–Siday–Aharonov–Bohm effect where interference occurs
between waves traversing two different physical pathways.
The QI antiresonance affects the tunneling conductance the most
when it is located near the energy of Fermi level of the electrodes
in the transmission spectra (i.e., in the frontier level gap of the
molecule). This position of antiresonance can be manipulated by
changing the electronic structure and conformation of the molecules
in the junction and can be further turned on and off
electrochemically, as I will demonstrate later in this
chapter.
3.3. THE BENCHMARKS: AC, AH, AND AQ SERIES First experimental
evidence of tunneling charge-transport manipulation via QI in
large- area MTJ was provided by Fracasso et al.[14] The authors
showed that the conduct- ance of molecular wires can be affected by
manipulating the bond-topology, thereby changing the conjugation.
They studied 3 molecular wires with the same anchoring groups
bearing different cores as shown in Figure 3.3a. The cores in AC
(anthracene;
4,4’-(anthracene-2,6-diylbis(ethyne-2,1-diyl))dibenzenethiol), AQ
(anthraquinone; 2,6-
bis((4-mercaptophenyl)ethynyl)anthracene-9,10-dione), and AH
(dihydroanthracene;
4,4’-((9,10-dihydroanthracene-2,6-diyl)bis(ethyne-2,1-diyl))dibenzenethiol)
introduce linear-, cross-, and broken-conjugation in the 3
molecular wires. Respectively, (i) AC has a continuous
single-double bond alternation from one terminal sulfur to the
other, (ii) AQ has two non-interacting sequences of single-double
bond alternation shown by different colors in Figure 3.1b, and
(iii) AH also has two non-interacting sequences of single-double
bonds that are bridged by two saturated methylene (–CH2–) groups
act- ing as sigma spacers. The authors calculated the geometric and
the gaussian means of current densities and deduced that the
low-bias conductance follows the trend as AC > AH > AQ. A
continuous delocalization of electron density due to the conjugated
bonds in linearly-conjugated AC makes it most conductive as shown
in Figure 3.3a. Break in the conjugation in AH core compared to the
AC results in lower tunneling conductance, while the lowest
conductance of AQ is ascribed to destructive QI that occurs near
the
3
51
INTERFERENCE
a b
-2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
100
AC AH AQ
Figure 3.3 (a) Semilog J −V plots showing geometric means (lines)
and Gaussian (µlog) means (symbols) for AC (solid line; squares),
AH (dotted line; triangles), and AQ (dashed line; circles). Both
statistical methods show that AC is clearly more conductive than
either AH or AQ, while meaningful distinction is difficult to make
for the latter two. Reprinted with permission.[14] Copyright 2011,
American Chemical Society. (b) Transmission spectra of AC, AH, and
AQ calculated using ORCA[65,66] and Artaios[67] showing high
conductance for linearly- conjugated AC and destructive QI dip for
AQ (at ≈ 0.25 eV). The trend in transmission probability at EFermi
shows qualitative agreement with the experimentally measured
conductance.
EFermi induced by the cross-conjugation in bond-topology. The
destructive QI effect in this series was also demonstrated later in
single-molecular junctions, and other experi- mental setups
(supported by theory).[30,50,51,60–64]
We performed DFT+NEGF simulations on gas-phase optimized geometries
of these three molecules using ORCA quantum chemistry software and
Artaios program for calculating the transmission spectra, following
the same procedure as described in chapter 2. The theoretical QI
signature can be seen in the transmission spectra of AQ in Figure
3.3b in form of a significant dip slightly below 0.25 eV. The
energy axis has been referenced to the energy of the Fermi level of
the EGaIn electrode.[68] The conduct- ance trend at E−EFermi = 0
qualitatively agrees with the experimental conductance trend
reported by Fracasso et al.: AC > AH > AQ.
A presence of electron-withdrawing quinone moiety in the core
localizes the charge density in the core. This can also be seen in
the Figure 3.4, where isoplot of the LUMO level shows charge
density localized in the core as opposed to AC which has uniformly
distributed charge density. The electron-withdrawing quinone moiety
also lowers the energy of LUMO level (−3.24 eV, compared to −2.37
eV for AC and −1.57 eV for AH) be- cause of the non-bonding level
originating from the carbonyl groups resulting in the smallest
optical bandgap in the series. Despite the smallest bandgap, the
presence of de- structive QI feature results in AQ being least
conductive. Carlotti et al., in their follow-up work, further
elucidate that the conduction in AH can be thought of as
"through-space" conduction compared to a "through-bond" conduction
in AC, which makes the former less conducting than the latter.[34]
The authors demonstrated through-space conduct- ance in AH, which
can further depend on the bend in the core of AH.
3.4. MOVING QI DIP BY FUNCTIONALIZING AQ As reported here and in
previous literature, the origin of destructive QI feature in AQ
SAMs is a result of both cross-conjugation[8,10,69] in the
bond-topology and the presence
3
52
3.4. MOVING QI DIP BY FUNCTIONALIZING AQ
Figure 3.4 Frontier molecular orbital isoplots HOMO and LUMO, and
HOMO−1 and LUMO+1 of AC, AH, and AQ (isovalue of 0.02) with
corresponding gas-phase orbital energies shown next to the orbital
diagrams.
of an electron-withdrawing quinone functional group.[70–72] Andrews
et al., using theor- etical simulations, showed that width, depth,
and entire location of the quantum inter- ference feature can be
changed via functionalization of cross-conjugated
molecules.[70]
In the case of AQ, the two carbonyl positions offer the possibility
of functionalization while preserving the cross-conjugated
bond-topology. Even though, as we will discuss further below, not
all the AQ derivatives are synthetically accessible, which we have
the- oretically investigated (Figure 3.1c). We can divide the
proposed AQ derivatives in this work in two separate categories:
(i) all-Carbon derivatives comprising AMe, APh, A(CH2), A(All), and
A(Alk); (ii) ones with heteroatoms in their core comprising ATTF,
TCNAQ, ABr, and AF. The classification will be more clear in this
section when we discuss the transmission spectra of these molecular
wires.
All the molecular wires studied in this part have identical
molecular skeletons and binding groups to the parent anthraquinone
wire (AQ),[14] but with different CR2 groups replacing the oxygen
in the carbonyl, thus changing molecular geometry, energies and
localization of the orbitals, and the distribution of electron
density, without altering the cross-conjugated core (Figure 3.1).
We investigated the electrical properties of SAMs of anthraquinoid
compounds with two different top electrodes (EGaIn and CP-AFM,
(AuAFM) and found that their conductance roughly follows the order
TCNAQ ≈ AC > ATTF > APh ≈ ABr > AQ. Other AQ derivatives
shown in Figure 3.1 were not synthet- ically accessible except AMe
which could be synthesized but did not form good SAMs, for unknown
reasons, as seen by HRXPS measurements.[49]
We simulated the transmission spectra for all the proposed
derivatives in Figure 3.5 clubbing the all-carbon derivatives and
the ones with heteroatoms in the core, separ- ately in two graphs
allowing easier comparison. As seen in Figure 3.5a, the all-Carbon
AQ derivatives split the QI feature into two separate dips
occurring just before the two transmission resonance peaks going
from EFermi (except for A(All)), in agreement with previously
reported transmission for A(CH2).[51]
3
53
INTERFERENCE
a
-2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
b
-2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
100
AQ ABr TCNAQ ATTF AF
Figure 3.5 Calculated transmission probability as a function of
electron energy (with respect to EGaIn’s EFermi = −4.3 eV[68]) of
different AQ derivatives. (a) all-carbon wires; (b) wires
containing herteroatoms. AQ is reported in both the plots as
reference.
Compared to the derivatives with heteroatoms, the electron-
donating/withdrawing ability of the functional groups in all-
carbon compounds is weaker. The resonance peaks (T(E)→ 1) for E
<EFermi is slightly lower compared to AC (Figure 3.3) and for E
>EFermi the peaks are about 1 eV higher in en- ergy, except for
A(Alk) which tracks with its low LUMO level, tabulated in Table
3.1. The lower LUMO of A(Alk) is a res- ult of the four sp
hybridized al- kyne groups having the strongest
electron-withdrawing inductive effect compared to their sp2 and sp3
analogues. The cumulative inductive effect results in lower LUMO
(and Eg , Table 3.1) as well as the interference feature be- ing
closer to EFermi (E−EFermi = 0.78 eV). The inductive effects
of
aryl derivative (APh) and sp3 derivative (AMe) are sequentially
smaller, resulting in LUMO being higher in energy and the
corresponding QI dip being at 1.65 eV and 1.73 eV, respectively.
The transmission spectra of A(CH2), on the other hand, is similar
to AMe but shifted lower in energies. A(Alk) does not show that big
of a shift since the double bonds are next to each other resulting
in orthogonal π-orbitals on the sp carbon. The ex- perimental
observation of reduced conductance of APh derivative compared to AC
and higher conductance compared to AQ can thus be supported using
these transmission calculations. A(All) is the only derivative that
doesn’t have a CR2 substitution at the car- bonyl position.
Instead, it introduces a cumulated diene with sp carbon of the
allene functional group instead of oxygen; in allenes, the carbons
at 1 and 3 positions are usu- ally considered non-conjugated, this
difference seems to result in the (QI) feature-less, suppressed
transmission spectrum of A(All). For instance, recently published
work by Venkataraman et al.[73] showed that sp-connected carbons in
cumulene behaves exactly the opposite of sp2-connected carbon
chains of polyyne when it comes to change in tunneling with
increasing lengths. With increasing length, tunneling current
increases and decreases for cumulene and polyyne, respectively. The
authors ascribe this to the reversed trend in bond length
alternation between cumulene and polyyne as well as the former
having smaller magnitude of bond length alternation. Their study
aids answering the question why A(All) having cumulene group
behaves differently than the rest of the AQ derivatives. The
orbital density localization of LUPS for A(All) is also similar to
the strong electron-donating ATTF derivative, discussed in the next
paragraph, in contrast
3
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3.4. MOVING QI DIP BY FUNCTIONALIZING AQ
Figure 3.6 Orthographic projections of Highest Occupied π-States
(HOPS) and Lowest Unoccupied π-States (LUPS) of several AQ
derivatives described in section 3.4 in metal-molecule single
molecule model system, along with AQ itself as a reference.
to the other all-Carbon derivatives.
Meanwhile, AQ derivatives with heteroatoms show a more prominent
change in be- havior of the QI feature, and transmission spectra in
general, as they affect the elec- tronics of the molecule wires
more strongly than the all-Carbon wires. TCNAQ with the well-known,
strong electron-withdrawing tetracyanoquinone(TCNQ)-based core
pulls the LUMO much lower in energy, even more than the carbonyls
in AQ, bringing the in- terference feature to −0.35 eV w.r.t. the
EFermi. The bigger effect can also be seen in the frontier orbital
plots shown in Figure 3.6. Compared to AQ, the LUPS has even higher
electron density localized in the core, while the HOPS has a
smaller electron density in the core and even smaller localization
in the phenylacetylene arms (compared to AQ). The
electron-withdrawing nature is so strong that the transmission
resonance peaks for E >EFermi sit right next to EFermi. On the
other hand, the strong electron-donating analogue ATTF shifts the
entire spectra to higher energies with the resonance peak for E
<EFermi at −1.15 eV away from EFermi without any QI feature in
the energy range of our interest. This is very small considering
the overestimation of Eg that accompan- ies the drawbacks of these
simulations. The DFT predicted HOMO and LUMO values in Table 3.1
are higher compared to most other derivatives. While LUPS seems to
be the dominating frontier level in TCNAQ, HOPS seems to have a
bigger effect on trans- mission at EFermi in the case of ATTF. As
seen from Figure 3.6, opposite to AQ, ATTF has HOPS with localized
electron density in the core and HOPS with localized density in the
phenylacetylene arms. The presence of these energy level proximity
to EFermi in the cases of TCNAQ and ATTF supports the experimental
observation of their higher conductance compared to the all-Carbon
APh and AQ, for which the EFermi sits in the center of the
HOMO-LUMO gap. Surprisingly, the halogenated derivatives – AF and
ABr – show featureless suppressed transmission where F, being more
electronegative, shifts the spectra to lower energies slightly more
than Br. Both halogens shift the frontier levels
3
55
INTERFERENCE
AQ AMe APh A(CH2) A(All) A(Alk) ABr ATTF TCNAQ AF LUMO (eV) −3.24
−1.72 −1.87 −2.05 −1.92 −2.79 −2.35 −1.91 −3.99 −2.21 HOMO (eV)
−5.98 −5.44 −5.48 −5.62 −5.44 −5.60 −5.80 −4.86 −6.19 −5.77
bandgap (eV) 2.74 3.72 3.61 3.56 3.52 2.80 3.45 2.94 2.20 3.56 φ
(degree, ) 0 47 47 (45) 27 0 38 47 (44) 36 36 31
Table 3.1 DFT calculated gas-phase HOMO, LUMO, frontier orbital
bandgaps and bend angles of the molecular cores (illustrated in
Figure 3.7) for the wires proposed in Figure 3.1. Values shown in
parentheses are from X-ray crystal structure obtained by Dr. M.
Carlotti.[49]
to lower energy but not as much as TCNAQ or AQ. The transmission
spectra near EFermi
are similar in magnitude to most of the all-Carbon derivatives. The
molecular orbitals in Figure 3.6 further show that the LUPS has
lower localization of electron-density in the core compared to AQ
and very delocalized HOPS spanning across the molecule.
-3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
100
Bent AQ Linear AQ
Figure 3.7 Calculated transmission probability as a function of
electron energy (with respect to EGaIn’s EFermi = −4.3 eV[68]) of
AQ in planar or linear conformation (red: linear AQ), and with a
bend angle of 47° in the core (green: Bent AQ).
Obtaining the crystal struc- tures of these molecules would give
the best insight into inter- molecular interactions and mo- lecular
assemblies in SAMs. In Table 3.1, we tabulate the DFT predicted
bend angles of the molecular cores and the ones obtained from X-ray
crystallo- graphy in the parentheses.[49]
The data shows that molecules with bulkier functional groups are
more bent due to steric crowding. It could be tempting to relate
the bent in geometry
with the presence and absence of a sharp QI dip near EFermi. To
verify this hypothesis we simulated transmission spectra of AQ,
which is inherently planar, by constraining AQ in a geometry with
bent angle of 47° – similar to APh and ABr. It can be seen from
Fig- ure 3.7 that the transmissions spectra are the same except for
the shift in the QI dip by ≈ 0.25 eV. It can be argued that
changing the bent in the core could alter the orbital overlap
across the arms and change the transmission. Furthermore, it should
be considered that in SAMs, the molecular geometries are perturbed
by environmental effects such as col- lective effects arising from
intermolecular interactions, presence of metal electrodes, de-
fects, thermal fluctuations, etc. The QI feature, therefore, will
be a result of an averaged distribution of geometries. Thus, by
combining our finding from the simulated spectra (Figure 3.7) and
keeping in sight the SAM complexity argument, we would like to
argue that perturbation in electronic properties by the functional
group substitutions affects the QI more than geometrical
fluctuations. This is also supported by the findings of So- lomon
et al.[8] wherein they demonstrated that while the change in
bond-topology and functional groups show a prominent shift in the
transmission spectra of acyclic systems, transmission spectra of
several geometries of the same molecule obtained via molecular
dynamics simulations do not affect the QI dip significantly and is
present in all the cases.
3
56
3.4.1. REDOX-ENABLED QI SWITCHING IN TCNAQ
a b
-3.0
-2.5
-2.0
-1.5
-1.0
-3.5
-3.0
-2.5
-2.0
-1.5
Voltage (V)
Figure 3.8 (a) Schematic showing SAM of TCNAQ in the cross-
conjugated quinoid form (top) which is reversibly switched to a
mixed- SAM in which a fraction of the molecules are reduced to a
linearly- conjugated, hydroquinoid form (bottom); the top
cross-conjugated neutral form gives rise to destructive QI with
lower conductance com- pared to the linearly-conjugated reduced
form. (b) Examples of log |J | vs. V traces of junctions comprising
SAMs of TCNAQ (top, black) show- ing significant hysteresis in
negative bias range, compared with AC as reference showing
overlapping forward and reverse traces (bottom, blue) on AuTS.
Solid dots represent (data acquired by Dr. M. Carlotti) five
forward scans going from −1.00 V to 1.00 V, while open dots repres-
ent data acquired during reverse scans from 1.00 V to −1.00
V.[43]
Unlike single-molecular techniques, SAM-based MTJ provide a viable
pro- spect as a technologic- ally relevant platform as they can be
up-scaled for manufacturing and en- capsulated in stable, static
devices.[26,48,74] As dis- cussed in earlier sections, QI lowers
the transmission probability between the electrodes, significantly
lowering tunneling con- ductance without altering the tunneling
distance.[35]
In our published work,[43]
we demonstrate a potential QI-based, two-terminal molecular memory
com- prising SAMs of TCNAQ: the AQ derivative with tet-
racyanoquinone (TCNQ) core, which is known to be a very
electron-withdrawing molecular moiety (also dis- cussed in section
3.4). The QI memory effect occurs due to active redox chemistry
between the Au electrode and strongly electron-withdrawing TCNQ.
The TCNQ core can reversibly switch between the two redox states
which have very different transmission probabilities of the
tunneling electrons in MTJ. Thus, in this section, we show how NEGF
calculations can be used to explain the difference in conductivity
using the different transmission spectra for the neutral and
doubly-reduced TCNAQ species.
Figure 3.8a shows a schematic of SAMs of TCNAQ which can be
switched (on several coinage metal substrates) between, and
addressed in, two conductance states (ON and OFF) in a two-terminal
proto-device using EGaIn top-contacts. We will show that the
different conductance states can be ascribed to the modulation of
the bond-topology of the molecule; TCNAQ—just like TCNQ—can readily
accept an electron from the bottom metallic substrate and form a
stable (di)anion that converts cross-conjugated pathways to
linearly-conjugated pathways, altering the transmission probability
similarly to inter- conversion of quinones and hydroquinones.[30] A
low-lying LUMO brings the reduction potential of TCNAQ close to the
oxidation potential of Au, Ag, and Pt electrodes, elimin- ating the
need for a third electrode or redox agent.
Example J−V traces are shown in Figure 3.8b where the black data
points for TCNAQ
3
57
INTERFERENCE
show very prominent, reproducible hysteresis between the forward
and the reverse traces. SAMs of TCNAQ readily accept an electron
from the Au electrode upon the forma- tion of self-assembly,
reducing a fraction of molecules to the hydroquinoid forms. When a
positive potential is applied on the EGaIn top electrode, the
reduced molecules are oxidized back to the neutral form which is
cross-conjugated, and hence, is lower in con- ductance due to QI
(open-symbols, reverse trace in Figure 3.8b). When a negative po-
tential is applied, a few molecules switch again to the reduced,
linearly-conjugated form with higher conductance (solid squares,
forward trace in Figure 3.8b), causing hyster- esis in every loop.
The blue curve in Figure 3.8b corresponds to J −V traces of
linearly- conjugated AC molecular wire (section 3.3), as a control,
which shows no hysteresis.
a
10-4
10-3
10-2
10-1
Efermi
b
-7 -6 -5 -4 -3 -2 -1 0 10-7 10-6 10-5 10-4 10-3 10-2 10-1 100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
ELUMO
ESUMO
Efermi
c
-7 -6 -5 -4 -3 -2 -1 0 10-7 10-6 10-5 10-4 10-3 10-2 10-1 100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
ELUMO
EHOMO
Efermi
d
-7 -6 -5 -4 -3 -2 -1 0 10-7 10-6 10-5 10-4 10-3 10-2 10-1 100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
ELUMOEHOMOEfermi
Figure 3.9 Transmission plots from uncorrected DFT calculations:
(a) Neut- ral TCNAQ; (b) The α spin channel of TCNAQ•– ; (c) TCNAQ2
– ; (d) The β
spin channel of TCNAQ•– . The black, vertical dashed line
corresponds to EFermi = −4.3 eV.[68] The electron configurations of
the frontier orbitals, rel- ative to neutral TCNAQ, are shown in
the insets. The uncorrected orbital en- ergies under-estimate the
HOMO/LUMO gap of TCNAQ and, due to the lack of counterions and
solvation, shift the orbitals of the reduced species close to
vacuum.
As discussed in the earlier section 3.4, TCNAQ is even more
electron-withdrawing than AQ, which results in QI dip being present
further lower on the energy scale of the transmission spectra, as
shown in Figure 3.5b. The frontier orbitals are also lower in
energy for TCNAQ compared to AQ, tabulated in Table 3.1. This trend
correlates with the transmission spectra as well where the peak (T
(E) → 1) for E > EFermi is lower in energy for TCNAQ than AQ.
Next, to elucidate the experimental redox- enabled memory effect,
we simulated transmis- sion spectra following
the single-point energy calculations on the singly- and
doubly-reduced TCNAQ species, denoted as TCNAQ•– and TCNAQ2 – ,
respectively.
We followed the same procedures for the calculations as mentioned
earlier. The Hamiltonian (Fock) and overlap matrices were generated
from the output of single-point energy calculations. In the case of
the radical anions, Hamiltonian matrices were gen- erated for both
the α and β spin states. The Hamiltonian and overlap matrices were
then used as inputs for Artaios-030417 to generate the transmission
curves using the non-equilibrium Green’s function.[67,75] This
method separates the finite cluster system into a bulk
calculation/approximation for the electrodes and a central
subsystem that
3
58
3.4. MOVING QI DIP BY FUNCTIONALIZING AQ
may or may not include some of the atoms from the electrodes. We
omitted the elec- trodes and computed the transmission between the
terminal sulfur atoms. As before, we chose EFermi value of −4.3
eV[68] to scale the E−EFermi energy axis. This value is both an
approximation of the work function of EGaIn[68] and the value of Au
modified with a thiol-SAM.[76]
a
10-4
10-3
10-2
10-1
EHOMO
ELUMO
Efermi
b
-7 -6 -5 -4 -3 -2 -1 0 10-7 10-6 10-5 10-4 10-3 10-2 10-1 100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
ESUMO Efermi
c
-7 -6 -5 -4 -3 -2 -1 0 10-6 10-5 10-4 10-3 10-2 10-1 100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
EHOMO ELUMO
10-4
10-3
10-2
10-1
100
Tr an
sm is
si on
P ro
ba bi
lit y
Energy (eV)
ESUMO Efermi
Figure 3.10 Transmission plots from DFT calculations corrected
using exper- imental values: (a) Neutral TCNAQ; (b) The α spin
channel of TCNAQ•– ; (c) Neutral TCNAQH2, the formally-reduced
hydroquinoid form of TCNAQ in which the cross-conjugation has been
deliberately broken by the addi- tion of H2; (d) The β spin channel
of TCNAQ•– . The energy-axis were shif- ted to align ELUMO and
ESOMO to their experimental values from cyclic voltammetry.[43]
EHOMO for TCNAQ was estimated by subtracting the on- set of the
reported UV-vis absorption (525 nm) from ELUMO obtained from
reported CV measurements;[43] for TCNAQH2 values were taken from
DFT, hence the large difference in Eg from the neutral TCNAQ. The
black, vertical dashed line corresponds to EFermi=−4.3 eV. The
electron configuration of the frontier orbitals relative to neutral
TCNAQ are shown in the insets. The cor- rected values place the
energies of ELUMO and ESOMO very close to EFermi, in agreement with
our proposed mechanism of switching. The sharp dip and depressed
transmission near EFermi for TCNAQ are absent for both spin
channels of TCNAQ•– , but the influence of the conjugation patterns
is more clearly resolved in the comparison between the two neutral
species, TCNAQ and TCNAQH2.
We omitted the electrodes because we could not capture the
collective effects of the SAM, particularly in a mixed-state of
neutral and reduced molecules. Thus, the energies of the orbitals
for the two anionic forms, TCNAQ•– and TCNAQ2 – were pushed very
close to vacuum due to the absence of electrodes, coun- terions,
solvation, and the near-by molecules that would be other- wise
present in a SAM. Figure 3.9 shows the physically unrealistic
result of these calcula- tions, which places un- occupied orbitals
below EFermi in some calcu- lations and occupied above EFermi in
others. The doubly-reduced species, TCNAQ2 – is particularly
illustrative, placing both frontier orbitals just below 0 eV.
To try to com- pensate for the unknowables and assumptions in these
model DFT calculations, we re-plotted the transmission curves using
experimental values taken from CV and UV-Vis data,[43] which
provide the energies of the LUMO and SOMO of TCNAQ and TCNAQ•–
(from CV) and the frontier orbital gap of TCNAQ (from UV-Vis), from
which the HOMO can be estimated. Note that this is a linear shift
that does not correct the under-estimated Eg, which would broaden
the dip near EFermi, but would not affect the interpretation of the
results. Figure 3.10 shows the results of these calculations,
3
59
INTERFERENCE
a
-5
-4
-3
-2
b
-2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
100
BDT1 BDT2 BDT3 AQ
Figure 3.11 (a) Plots of log |J (Acm−2)| versus V of Au/SAM//EGaIn
junctions comprising SAMs of BDT-1 (green), BDT-2 (red), BDT-3
(blue) and AQ (black). Each datum is the peak position of a
Gaussian fit of log |J | for that voltage. The error bars are 95 %
confidence intervals taking each junction as a degree of freedom.
(b) Transmission spectra for isolated molecules of BDT-n and AQ.
The spectrum of BDT-1 is featureless between the resonances
(transmission→ 1) near the frontier orbitals. The sharp dips in the
spectra of BDT-2, BDT-3 and AQ are destructive QI features. The
energies on the bottom axis are with respect to the EFermi value of
EGaIn at −4.3 eV.
which place the LUMO and SOMO orbitals very close in energy to
EFermi. The loss of the suppressed transmission and sharp dip near
EFermi for TCNAQ is evident in both the α and β spin channels of
TCNAQ•– . We interpret this difference as the loss of QI when the
cross-conjugated core of TCNAQ is replaced by the
linearly-conjugated core that is expected to be (by far) the
dominant resonance structure of TCNAQ•– , however, the introduction
of unpaired spins strongly affects the features of the transmission
plots. Thus, we also plotted the formally reduced, but neutral
hydroquinoid form, TCNAQH2, in which the cross-conjugation is
deliberately removed by the addition of H2. The comparison between
TCNAQ and TCNAQH2 clearly highlights the role of conjugation
patterns. Taken together, the data in Figure 3.10 support our
proposed mechanism, which localizes spin and charge on the central
carbons of the malononitrile substituents, favoring the
re-aromatization of the anthracene core.
3.5. BDT SERIES: EFFECT OF QUINONE ON QI Experimental studies on
conjugation patterns other than AC/AQ are currently lim- ited to
ring substitutions such as meta-substituted phenyl rings,[17–24] or
varied con- nectivity in azulene.[25–27] These molecular systems
differ fundamentally[2,8,32,38,46] from cross-conjugated bond
topologies[30,77,78] because they change tunneling pathways or
molecular-lengths or bond-topology, simultaneously. Isolating these
variables is how- ever important because the only primary
observable is conductance, which varies ex- ponentially with
molecular length. More recent work has focused on “gating” QI
effects by controlling the alignment of π-systems
through-space[32–34] and affecting the orbital symmetry of aromatic
rings with heteroatoms.[29,39,40] These studies exclusively invest-
igate the effects of the presence and absence of QI features; to
date—and despite recent efforts[79]—the specific effects of
bond-topology and electronegativity on the depth and position of QI
features have not been isolated experimentally.
In this section, I will discuss our work[80] where we demonstrate
that the electron-
3
60
3.5. BDT SERIES: EFFECT OF QUINONE ON QI
Figure 3.12 Molecular orbital isoplots of BDT-1, BDT-2, and BDT-3
for isovalue of 0.02 with corresponding gas-phase orbital energies
shown next to the orbital diagrams.
withdrawing quinone group in AQ and the cross-conjugated
bond-topology of AQ sep- arately influence the destructive QI
feature. Stressing on the fact that, ‘while cross- conjugation can
induce QI, quinone groups (among other electron-withdrawing groups)
pull it closer to EFermi’. To understand this further, we
introduced the new BDT-n series in Figure 3.4d, where we compare
two structurally similar isomers, changing the position of one of
the two S atoms, converting the molecule from linearly- to cross-
conjugated, reducing the overall tunneling current. Dr. Y. Zhang
and Dr. G. Ye de- signed and synthesized the series of
benzodithiophene derivatives: benzo[1,2-b:4,5- b’]dithiophene
(BDT-1, linearly conjugated),
benzo[1,2-b:4,5-b’]dithiophene-4,8-dione (BDT-2, cross-conjugated
with quinoid core), and benzo[1,2-b:5,4-b’]dithiophene (BDT- 3,
cross-conjugated without quinone, and an isomer of BDT-1). These
compounds isol- ate the influence of cross-conjugation
(bond-topology: BDT-1↔BDT-3) from that of the electron-withdrawing
effects of the quinone functionality (BDT-1↔BDT-2↔BDT- 3) while
controlling for the molecular formula and length. The variation in
the end- to-end lengths of these compounds is within 1 Å and the
linear- and cross-conjugated compounds BDT-1 and BDT-3,
respectively, differ only by the relative position of sul- fur
atoms. This series helps us to study the effect of
cross-conjugation and electron- withdrawing group independently,
unlike in AQ. Here we show, how with the help of DFT and transition
voltage spectroscopy, that the cross-conjugation introduces QI dip
while carbonyl groups move it closer to EFermi.
The J −V data for the BDT-n series and AQ are plotted in Figure
3.11a, showing that cross-conjugation lowers the conductance of
BDT-3 by an order of magnitude compared to BDT-1 but the quinone
functionality of BDT-2 and AQ lowers it further by another order of
magnitude, latter being in agreement with the analogous behavior of
AC and AQ.[14,51] The simulated transmission spectra of the four
molecules are shown in Fig- ure 3.11b. The linearly conjugated
BDT-1 is featureless with high transmission, identical to AC in
Figure 3.3. BDT-3 (the cross-conjugated isomer of BDT-1) has lower
transmis- sion compared to BDT-1 with a destructive QI dip at −2
eV, quite far away from EFermi.
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INTERFERENCE
The destructive QI dip of BDT-2 on the other hand is very close to
EFermi and has same shape of the curve as AQ. Further it can be
seen from Figure 3.12 that the DFT calculated frontier energy
levels of BDT-2 are lower in energy than BDT-1 and BDT-3, same as
AQ. The localization of the LUMO at the core of the molecule is
also similar to that of AQ, as seen from Figure 3.4. This shows
that the presence of an electron-withdrawing quinone group pulls
the frontier orbitals lower in energy and subsequently the QI dip
closer to EFermi. Because of the proximity of the QI dip to the
EFermi, its effect on the conductance is more significant than in
the case of BDT-3 where the QI dip is far away. The theoret- ically
predicted transmission spectra, performed on single-MTJ, thus
agrees remarkably with the experimentally observed tunneling
conductance from MTJ comprising SAMs, exhibiting the low-bias
conductance trend: BDT-1 > BDT-3 > BDT-2 ≈ AQ.
-2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 10-5
10-4
10-3
10-2
10-1
100
BDT-1 BDT-2 BDT-3 BDT-1F BDT-2CH2 BDT-2S
Figure 3.13 Transmission probabilities of BDT-1, BDT-2, and BDT- 3
along with their derivatives BDT-1F , BDT-2S, BDT-2C H2 as a
function of the energy of tunneling electron.
Many molecules can be difficult to synthesize, but in- silico
simulations provide us with tools to investigate as many variations
only limited by our creativity. Similar to the AQ derivatives
described in section 3.4, we studied 3 derivatives of BDT-n series:
linearly-conjugated BDT-1F containing two F atoms at the two
benzylic positions of BDT-1; quinoid, cross-conjugated BDT- 2S
containing S atoms instead of
O in BDT-2; quinoid, cross-conjugated BDT-2C H2 with two CH2 groups
instead of O in BDT-2. The transmission spectra are shown in Figure
3.13 and the molecular orbital diagrams with the energies of the
gas-phase frontier levels are shown in Figure 3.14. BDT-1F slightly
shifts the transmission spectra compared to BDT-1 to lower energies
and also the frontier orbitals showing the influence of the
electron-withdrawing fluorine groups on the linearly-conjugated
molecules. BDT-2C H2 on the other hand has two split QI dips just
like the all-carbon AQ derivatives discussed earlier in the
chapter. BDT-2S pulls the QI dip further down in energy just like
AQ derivatives functionalized with strong electron-withdrawing
groups. The effect is also evident from the molecular orbital plots
in Figure 3.14 where LUMO of BDT-2S, which is the dominant frontier
level participating in charge transport has similar localization of
electron density as BDT-2 but with higher density on the sulfur
atoms compared to oxygen atoms and the same in the rest of the
orbitals. These calculations show the flexibility and opportunities
that these molecular systems offer us to study and utilize QI as a
feature for potential molecular electronic devices.
To demonstrate that the intrinsic molecular properties are
preserved when the mo- lecule is attached between two metal
clusters, we compare the isoplots of the dominant gas-phase HOMO or
LUMO orbitals with the Highest Occupied π-State (HOPS) or Low- est
Unoccupied π-State (LUPS) in the MTJ in Figure 3.15. HOPS and LUPS
correspond to those “frontier" orbitals in these
metal-molecule-metal systems in which the majority
3
62
3.5. BDT SERIES: EFFECT OF QUINONE ON QI
Figure 3.14 Molecular orbital isoplots of BDT-n derivatives for
isovalue of 0.02 with corresponding gas-phase orbital energies
shown next to the orbital diagrams.
Figure 3.15 Frontier molecular orbital isoplots of BDT series
(isovalue of 0.02) showing both gas-phase mo- lecular orbitals
(HOMO/LUMO) and in presence of electrodes (HOPS/LUPS).
of orbital density is localized on the molecules and not the metal
electrodes. It is evident that the orbital coefficients and
symmetry are preserved in these calculations.
3.5.1. FUSED THIENOTHIOPHENE MOLECULAR WIRES. As an extension to
our above findings with the BDT series, we further studied molecu-
lar wires with fused thienothiophene rings in the core. The
molecular structure of TT- 1, TT-2, and TT-3, along with the
linearly-conjugated reference molecule BT is shown in Figure 3.1.
All TT-n (n = 1− 3) molecular wires are structural isomers of each
other where the only thing that changes is the position of the two
sulfur atoms, along with the connectivity of “arms” in TT-3. This
makes TT-1 linear-conjugated, while TT-2 and TT-3 cross-conjugated
with one and two cross-conjugated double bonds in TT-2 and TT-3,
re- spectively. Unlike BDT-n series, these molecules are devoid of
any quinone functionality and help us independently investigate the
effect of bond-topology and heteroatoms on QI. While TT-1 and TT-2
can be considered analogous to BDT-1 and BDT-3, respectively, TT-3
offers a different topological pattern, wherein, the single-double
bond alternation is broken twice highlighted by blue and red double
bonds in Figure 3.1e. If the involvement of the heteroatoms is
ignored in the core, TT-2 and TT-3 can be considered equivalent to
a cross-conjugated alkene with 1 and 2 nodes, respectively.
Large-area SAM based J −V measurements using EGaIn as a top
electrode and CP-
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INTERFERENCE
AFM were performed by Dr. Y. Zhang and Dr. X. Qiu, respectively,
while single-molecule MCBJ measurements were performed by Hong et
al. at Xiamen University. In all three experimental platforms, the
obtained conductance trend was TT-1 > BT > TT-2. After the
experiments were already performed, Dr. G. Ye also proposed TT-3
molecular wire. The synthesis and measurements of TT-3 are yet to
be performed, however, that doesn’t stop us from already predicting
the plausible transmission behavior of TT-3 in silico. The trend in
optical bandgap (Eg ) obtained from UV-Vis spectroscopy is BT (2.76
eV) < TT-1 (2.98 eV) < TT-2 (3.26 eV) following the same
trend as predicted by DFT: BT (2.82 eV) < TT-1 (3.01 eV) <
TT-2 (3.59 eV). The trend in experimentally observed conductance
does not follow Eg , suggesting that the tunneling change between
the wires is not just a simple band-gap effect.
-2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 10-5
10-4
10-3
10-2
10-1
100
BT TT-1 TT-2 TT-3
Figure 3.16 Transmission probability as a function of energy of the
tunneling electron for isolated molecules of TT-1, TT-2, and TT-3
molecules with reference to the control molecule BT. The sharp dip
in the spectrum of TT-2 is the destructive QI feature.
On the other hand, the trans- mission spectra obtained using DFT
(using ORCA quantum chemistry package[65,66]) + NEGF (using
Artaios[67]) sim- ulations, shown in Figure 3.16, exactly
reproduces the experi- mentally observed trend. Just like AC and
BDT-1 molecular wires, the linearly-conjugated BT and TT-1 show
featureless spectra with bowl-shaped trans- mission spectra between
the two resonances (transmission→ 1) around the HOMO and LUMO
energies. The cross-conjugated TT-2 shows a sharp QI dip at ≈ 1.9
eV. This QI dip even though is far away from EFermi is also
accompanied by a reduction in transmis- sion probability around
EFermi. This cross-conjugated induced QI dip results in the reduced
conductance of TT-2. These calculations also explain why the
conductance of TT-2 molecular wire is only 1 order of magnitude
lower than TT-1; compared to the benchmark AQ whose QI dip is
closer to EFermi and the experimental conductance is about 2 order
of magnitude lower than AC, its linear analogue (section 3.3).[49]
The takeaway from this series so far is the same as that from the
other series discussed earlier. However, TT-3 is a unique molecule,
as it now helps us study another molecule with same chemical
formula but with different connectivity. As pointed out earlier,
TT-3 has two cross-conjugated nodes. As can be seen in Figure 3.16,
TT-3 shows the transmission further suppressed but without the
presence of any QI feature. This is in agreement with the reported
transmission spectra by Andrews et al.,[70] (if the presence of
heteroatoms is ignored) where the addition of multiple
cross-conjugated nodes re- duce the transmission systematically.
Our systems present the advantage of conserving the molecular
geometry across the entire series and selectively studying the
effect of bond-topology on QI. If the future performed experiments
agree with the transmission trend at EFermi in Figure 3.16 – TT-1
> BT > TT-2 > TT-3 – these insights gained on the role of
heteroatoms will be useful from these thieonthiophenes for
designing molecules
3
64
3.6. CONCLUSIONS Combined with ab-initio Density Functional Theory
calculations & Non-equilibrium Green’s Function approach on the
model single-molecule tunneling junctions, we estab- lish
structure-function relationship. We have shown that manipulating
bond-topology and functional group effects on QI can be utilized to
elucidate conductance fluctuations across series of molecules
observed in large-area based MTJ. Without performing ex- cruciating
DFT simulations on periodic systems, or molecular dynamics
simulations on self-assembled monolayers, we show that
single-molecule models can be used to draw excellent qualitative
agreements with experimental observations, apart from acting as
crucial support behind the laid hypotheses.
Establishing the origin of QI in linear- and cross-conjugated
systems, we have estab- lished that the relative effects of QI on
tunneling conductance can be tuned by substi- tuting
cross-conjugated molecules, such as AQ with several
electron-withdrawing and donating functional groups. We have
investigated molecules in silico that are other- wise synthetically
inaccessible. We have shown that we can vary the position, width
and depth, and even split the QI feature by functionalization of AQ
with groups such as CN, TTF, F, Br, Ph, CH2, CH3, etc. Strong
electron-withdrawing tetracyanoquinone containing TCNAQ was also
shown to act as a molecular switch, switching between mul- tiple
redox states that enable effective QI switching for two-terminal
molecular memory application, explained using DFT+NEGF
simulations.
We further secluded the effects of bond-topology and quinone on
destructive QI by investigating tunneling transmission in BDT-n
SAMs. We conclusively demonstrated that while destructive QI is
induced in cross-conjugated systems, the presence of a strong
electron-withdrawing quinoid core brings the feature next to
EFermi, prominently affecting its conductance. This was
consequently verified in the thieonthiophene series where we could
study two isomers that preserve the molecular formula but change
the bond-topology from linear to cross-conjugation, making the
latter less conductive than the former due to destructive QI. In
another isomer of the thieothiophene series, we also studied
transmission that could provide insight into the role of S as a
heteroatom in mo- lecular wires, incorporating more than one
cross-conjugated node in the bond-topology.
3.6.1. OUTLOOK Finally, in all the molecules discussed above,
especially the AQ derivatives, the two path- ways in the molecules
are always similar (in terms of conjugation pattern) formed by
either two linearly-conjugated pathways in case of AC, or two
broken-conjugated in AH, or two cross-conjugated pathways in AQ
(including the derivatives). We have discussed how to manipulate QI
by functionalizing the two pathways symmetrically. However, the
presence of two different physical pathways opens the possibility
of studying different intramolecular pathways in parallel. I will
discuss a molecular wire system based on a fluorenone core that
lets us study the effects of parallel pathways with varying
conjuga- tion on QI in the next chapter.
3
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